Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil

Comparison between grapevine leaf and inflorescence upon downy mildew infection, based on a new in vitro phenotyping method

Downy mildew (DM), caused by the oomycete Plasmopara viticola (Berk. & Curt.) Berl. & de Toni, is one of the most important plagues affecting viticulture, especially in temperate-humid climates. P. viticola reduces fruit quality and yield, either by direct infection of berries or as a result of the reductions in photosynthesis and plant vigor caused by leaf infections. DM control is based on the repeated and massive use of fungicides, leading to problems such as environmental pollution, development of resistance and residual toxicity. The use of grapevine varieties showing durable resistance to DM is an alternative and promising strategy to control the disease. Nevertheless, most of the in vitro tests developed so far for DM resistance assessment are focused on leaf disk bioassays that not always represent a proper evaluation and prediction of the disease impact on grapevine inflorescence/bunch and therefore on final yield and wine quality. In this work, we firstly improved the annotation procedure of foliar resistance/susceptibility under controlled conditions (optimized OIV descriptor 452-1). Secondly, we developed a new in vitro phenotyping method - from infection to symptom evaluation - for DM resistance assessment on grapevine inflorescence, identifying the most responsive phenological stage (developed and proposed OIV descriptor 453-1). Thus, at this stage we screened several genotypes, in parallel with the optimized leaf disk bioassay, to compare the different pathogen responses between leaf and inflorescence collected from plants in untreated field. Finally, we validated our results performing the same DM resistance assessment also on organs detached from fruiting cuttings grown in phytotrone. Our optimized fruiting cutting agronomic technique turned out to be crucial for the anticipation of the study of late traits under controlled conditions

R-Loci arrangement versus downy and powdery mildew resistance level: a Vitis hybrid survey

For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breedin

Development of a novel phenotyping method to assess downy mildew symptoms on grapevine inflorescences

Grapevine downy mildew (DM), caused by the oomycete Plasmopara viticola (Berk. & Curt.) Berl. & De Toni, is one of the most important plagues affecting viticulture, especially in temperate rainy climates. P. viticola reduces fruit quality and yield, either by direct infection of berries or as a result of the reduction in photosynthesis and plant vigor caused by leaf infections. DM control is based on the repeated and massive use of fungicides, leading to problems such as environmental pollution, development of resistance and residual toxicity. The use of varieties showing durable resistance to DM is an alternative and promising strategy to control the disease. Nevertheless, most of the lab tests developed so far for DM resistance assessment are focused on leaf disc bioassays. This led us to consider that these tests might not always represent a proper evaluation and prediction of the disease symptom extent on inflorescences/bunches and therefore on final yield and grape/wine quality. Therefore, based on the screening of nine Vitis hybrids, we developed a new lab phenotyping method to assess the disease extent on inflorescences at flower button phenological stage, along with a novel annotation descriptor. Secondly, we combined this approach with the optimized leaf disc bioassay and found a general positive correlation between organ DM resistance phenotypes. Finally, we found that Cabernet Cortis could be a model to study DM divergent dual (on leaf and inflorescence) epidemics

Marker-assisted breeding for Downy mildew, Powderey mildew and Phylloxera resistance at FEM

Il programma di miglioramento genetico per le resistenze a stress biotici ha avuto inizio presso la Fondazione Edmund Mach (FEM) nel 2010. Inizialmente è stata condotta una caratterizzazione sia genotipica che fenotipica di materiali acquisiti da altri programmi di breeding e di materiale selvatico raccolto in New Jersey. Sia i genotipi conosciuti nei database internazionali che i genotipi sconosciuti, imparentati e non, sono stati impiegati come linee parentali nel processo di introgressione e di piramidazione di loci di interesse. Una volta pianificati e ottenuti gli incroci, la valutazione delle progenie è avvenuta seguendo un processo di Marker-Assisted Selection: dapprima è avvenuta la selezione fenotipica in serra in base al tipo di malattia e al numero di loci attesi per la medesima malattia; successivamente si è proceduto con lo screening molecolare in base ai loci specifici attesi nei parentali. Cinque sono i loci Run/Ren associati alla resistenza all’oidio presenti nel programma FEM; riguardo ai loci associati alla resistenza alla peronospora, quattro Rpv sono ben rappresentati nel piano di incroci. Ad oggi il 26% delle F1 è piramidizzato per quattro loci di resistenza.The genetic improvement program for resistance to biotic stresses began at the Edmund Mach Foundation (FEM) in 2010. Initially, both genotypic and phenotypic characterization of materials acquired from other breeding programs and wild material collected in New Jersey was conducted. Both the genotypes known in the international databases and the unknown genotypes, both related and unrelated, were used as parental lines in the process of introgression and pyramiding of loci of interest. Once the crossbreeds were planned and obtained, the evaluation of the progeny took place following a Marker-Assisted Selection process: at first the phenotypic selection in the greenhouse occurred based on the type of disease and the number of loci expected for the same disease; then we proceeded with molecular screening based on the specific loci expected in the parental groups. Five Run/Ren loci are associated with the resistance to powdery mildew present in the FEM program; with respect to the loci associated with the downy mildew resistance, four Rpv loci are well represented in the crossing plan. To date, 26% of F1 is pyramided for four resistance loci

Breeding for grapevine downy mildew resistance: a review of “omics” approaches

Downy mildew (DM) is one of the most destructive diseases affecting viticulture, especially in temperate-humid climates. This pathogen is able to differentially attack leaves and grapes, and is currently controlled with repeated applications of fungicides that lead to environmental pollution, development of resistant strains, residual toxicity, and pathogen pressure. The use of resistant grapevine varieties, obtained through breeding programs, represents a potential alternative to control grapevine DM, although this approach is constrained by the limits of natural resistance. In this review, we describe the latest breakthroughs achieved in the exploitation of the host–pathogen interaction, which have led to the identification of DM resistance loci, with associated molecular markers, that can be employed to efficiently screen hybrid grapevines and improve (pre-)breeding programs. The development of controlled infection protocols and contemporary “omics” approaches (next generation sequencing/genomics, QTLomics, transcriptomics, proteomics and metabolomics) integrated with comparative studies are shedding light onto the early host responses to DM attack and the complex plant defence mechanisms that are triggere

A new in vitro phenotyping method for Plasmopara viticola resistance assessment on grapevine bunches

Grapevine downy mildew (DM), caused by the biotrophic oomycete Plasmopara viticola (Berk. & Curt.) Berl. & de Toni, is one of the most important plagues affecting viticulture, especially in humid climates. This pathogen is able to differentially attack leaves and grapes and is currently controlled with the massive use of fungicides, which has considerable economic costs as well as a relevant negative impact on environment, human health, and public perception. The use of resistant grapevine varieties, obtained through breeding programs, is a cost-efficient way to control grapevine DM. Most of the in vitro tests developed so far for DM resistance assessment are focused on leaf disk bioassays. This led us to consider that these tests might not always represent a proper evaluation and prediction of the disease impact on grape bunches and therefore on final production and quality. At first different experimental tests were carried out on the bunch to develop a new infection and phenotyping method. At a later stage this method was applied to screen several genotypes, in parallel with the traditional leaf disks phenotyping approach. In this way we were able to compare the different responses to the pathogen between leaf and bunch collected in untreated field. Here we present the detailed protocol that will be applied on some specific genotypes of interest to investigate whether the plant-pathogen interaction is organ-specific

A new in vitro method for the assessment of Plasmopara viticola resistance on grapevine inflorescences

Grapevine downy mildew (DM), caused by the pathogen Plasmopara viticola, is one of the most important plagues affecting viticulture, especially in humid climates. This pathogen is able to differentially attack leaves and grapes and is currently controlled with a massive use of fungicides; the numerous treatments have considerable economic costs as well as a relevant negative impact on environment, human health and public perception. The use of resistant grapevine cultivars, obtained through breeding programs, is a cost-efficient way to control grapevine DM. Nevertheless, most of the in vitro tests developed so far for DM resistance assessment are focused on leaf disc bioassays. These tests might not always represent a proper evaluation and prediction of the disease impact on grape inflorescences/bunches and in turn on final production and qualit